6T28

Crystal structure of human calmodulin-dependent protein kinase 1D (CAMK1D) bound to compound 19 (CS640)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.157 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Discovery of Highly Selective Inhibitors of Calmodulin-Dependent Kinases That Restore Insulin Sensitivity in the Diet-Induced Obesityin VivoMouse Model.

Fromont, C.Atzori, A.Kaur, D.Hashmi, L.Greco, G.Cabanillas, A.Nguyen, H.V.Jones, D.H.Garzon, M.Varela, A.Stevenson, B.Iacobini, G.P.Lenoir, M.Rajesh, S.Box, C.Kumar, J.Grant, P.Novitskaya, V.Morgan, J.Sorrell, F.J.Redondo, C.Kramer, A.Harris, C.J.Leighton, B.Vickers, S.P.Cheetham, S.C.Kenyon, C.Grabowska, A.M.Overduin, M.Berditchevski, F.Weston, C.J.Knapp, S.Fischer, P.M.Butterworth, S.

(2020) J Med Chem 63: 6784-6801

  • DOI: https://doi.org/10.1021/acs.jmedchem.9b01803
  • Primary Citation of Related Structures:  
    6T28, 6T29

  • PubMed Abstract: 

    Polymorphisms in the region of the calmodulin-dependent kinase isoform D (CaMK1D) gene are associated with increased incidence of diabetes, with the most common polymorphism resulting in increased recognition by transcription factors and increased protein expression. While reducing CaMK1D expression has a potentially beneficial effect on glucose processing in human hepatocytes, there are no known selective inhibitors of CaMK1 kinases that can be used to validate or translate these findings. Here we describe the development of a series of potent, selective, and drug-like CaMK1 inhibitors that are able to provide significant free target cover in mouse models and are therefore useful as in vivo tool compounds. Our results show that a lead compound from this series improves insulin sensitivity and glucose control in the diet-induced obesity mouse model after both acute and chronic administration, providing the first in vivo validation of CaMK1D as a target for diabetes therapeutics.


  • Organizational Affiliation

    Centre for Biomolecular Sciences and School of Pharmacy, University of Nottingham, Nottingham NG7 2RD, U.K.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Calcium/calmodulin-dependent protein kinase type 1DA [auth AAA]385Homo sapiensMutation(s): 0 
Gene Names: CAMK1DCAMKID
EC: 2.7.11.17
UniProt & NIH Common Fund Data Resources
Find proteins for Q8IU85 (Homo sapiens)
Explore Q8IU85 
Go to UniProtKB:  Q8IU85
PHAROS:  Q8IU85
GTEx:  ENSG00000183049 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8IU85
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
M92 (Subject of Investigation/LOI)
Query on M92

Download Ideal Coordinates CCD File 
H [auth AAA]2-[(3~{S})-3-azanylpiperidin-1-yl]-4-[[2,6-di(propan-2-yl)pyridin-4-yl]amino]pyrimidine-5-carboxamide
C21 H31 N7 O
BWBUPDTUXQDHSX-AWEZNQCLSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
B [auth AAA],
F [auth AAA],
G [auth AAA]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
EDO
Query on EDO

Download Ideal Coordinates CCD File 
C [auth AAA],
D [auth AAA],
E [auth AAA]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
M92 BindingDB:  6T28 IC50: min: 8, max: 11 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.157 
  • Space Group: I 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.64α = 90
b = 45.62β = 104.439
c = 108.949γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom202708

Revision History  (Full details and data files)

  • Version 1.0: 2019-11-13
    Type: Initial release
  • Version 1.1: 2020-07-01
    Changes: Database references, Structure summary
  • Version 1.2: 2020-07-22
    Changes: Database references
  • Version 1.3: 2024-01-24
    Changes: Data collection, Database references, Derived calculations, Refinement description